Contacts of the helix formed by residues 431 - 455 (chain B) in PDB entry 5YD6
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 431 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B ASP 4.2 2.9 - - - +
430B LEU* 1.4 85.8 - - + +
432B LYS* 1.3 67.2 + - - +
433B ALA* 4.3 5.2 - - + +
434B ASP* 2.8 34.4 + - - +
435B GLN 3.0 9.5 + - - -
519B LYS* 4.2 20.4 - - + +
520B GLU* 3.7 35.0 - - + +
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Residues in contact with LYS 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B ARG* 5.0 10.5 - - - +
422B GLU* 5.5 5.3 + - - -
430B LEU 3.4 2.2 + - - -
431B PRO* 1.3 70.1 - - - +
433B ALA* 1.3 56.6 + - - +
435B GLN* 3.1 27.7 + - + +
436B ASP* 2.9 60.4 + - - +
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Residues in contact with ALA 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B PRO* 3.1 1.7 - - + +
432B LYS* 1.3 78.3 - - - +
434B ASP* 1.3 59.8 + - - +
436B ASP* 3.7 9.7 + - - +
437B LEU* 3.0 27.2 + - - +
519B LYS* 3.8 35.9 - - + +
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Residues in contact with ASP 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B LEU* 4.1 16.2 - - + +
431B PRO* 2.8 26.4 + - + +
433B ALA* 1.3 75.7 - - - +
435B GLN* 1.3 60.3 + - - +
437B LEU* 3.7 2.3 - - - +
438B LEU* 2.9 37.8 + - - +
517B GLY 4.3 2.4 - - - +
518B LEU* 3.5 22.7 - - + +
519B LYS* 2.7 30.7 + - - +
520B GLU* 2.9 31.5 + - - +
524B VAL* 5.1 0.5 - - - +
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Residues in contact with GLN 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B GLU* 4.2 17.8 + - - +
427B PHE* 3.4 57.2 - - + +
428B ALA* 3.7 18.0 - - - +
430B LEU* 2.9 22.5 - - + +
431B PRO 3.0 10.0 + - - +
432B LYS* 3.1 30.2 + - + +
434B ASP* 1.3 77.4 - - - +
436B ASP* 1.3 57.7 + - - +
438B LEU 3.4 0.2 + - - -
439B PHE* 2.9 34.0 + - - +
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Residues in contact with ASP 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B ARG* 4.6 10.9 + - - +
432B LYS* 2.9 53.2 + - - +
433B ALA* 3.8 8.0 - - - +
435B GLN* 1.3 71.6 - - - +
437B LEU* 1.3 64.3 + - - +
439B PHE* 4.0 3.5 - - - +
440B GLU* 2.9 50.3 + - - +
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Residues in contact with LEU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B ALA 3.0 17.5 + - - +
434B ASP* 3.7 5.4 - - - +
436B ASP* 1.3 80.3 - - - +
438B LEU* 1.3 56.1 + - - +
440B GLU* 4.2 4.4 - - + +
441B SER* 2.9 48.4 + - - +
515B ARG* 4.2 12.3 - - + -
516B HIS 3.5 22.7 - - - +
517B GLY* 3.5 29.8 - - - +
518B LEU* 3.7 17.7 - - + +
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Residues in contact with LEU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B PHE* 3.8 13.7 - - + -
430B LEU* 3.5 32.3 - - + -
434B ASP 2.9 20.8 + - - +
435B GLN 3.9 2.7 - - - +
437B LEU* 1.3 70.8 - - - +
439B PHE* 1.3 66.4 + - - +
441B SER* 4.0 3.5 - - - -
442B ALA* 3.3 25.3 + - - +
511B MET* 3.5 27.6 - - + +
512B VAL* 4.8 6.7 - - + -
513B THR 3.4 25.8 - - - +
515B ARG* 4.0 9.9 + - + -
518B LEU* 3.9 18.4 - - + -
524B VAL* 4.0 15.9 - - + -
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Residues in contact with PHE 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B MET* 3.4 37.0 - - + -
417B ILE* 3.6 23.1 - - + -
418B ARG* 3.4 70.7 - - + +
421B ALA* 4.7 1.8 - - + -
427B PHE* 4.7 4.5 - - + -
435B GLN 2.9 21.2 + - - +
436B ASP* 4.0 1.8 - - - +
438B LEU* 1.3 72.7 - - - +
440B GLU* 1.3 68.2 + - + +
442B ALA* 3.3 1.7 + - - +
443B PHE* 2.8 44.9 + + + -
446B LEU* 4.9 0.5 - - - +
511B MET* 3.8 19.9 - - - +
591B LEU* 4.9 2.0 - - + -
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Residues in contact with GLU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B ARG* 4.3 8.3 + - - +
436B ASP* 2.9 41.8 + - - +
437B LEU* 4.2 4.2 + - + +
439B PHE* 1.3 89.0 - - + +
441B SER* 1.3 60.0 + - - +
443B PHE* 3.6 4.6 + - - +
591B LEU* 3.6 35.5 - - + +
594B ASP* 6.1 1.0 - - - +
595B THR* 5.4 4.9 - - - +
601B 8SU 2.9 33.9 + - - +
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Residues in contact with SER 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B LEU* 2.9 37.9 + - - +
438B LEU 4.0 0.9 - - - -
439B PHE 3.4 0.2 - - - -
440B GLU* 1.3 76.7 - - - +
442B ALA* 1.3 57.5 + - - +
445B GLU* 3.7 11.6 - - - +
515B ARG* 3.4 35.2 + - - -
595B THR* 5.9 1.8 - - - -
601B 8SU 3.3 42.4 - - - +
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Residues in contact with ALA 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B LEU 3.3 17.2 + - - +
439B PHE 3.6 0.4 - - - +
440B GLU 3.2 0.4 - - - -
441B SER* 1.3 77.6 - - - +
443B PHE* 1.3 65.6 + - - +
444B LEU 3.4 2.2 - - - -
445B GLU* 3.1 12.7 + - + +
446B LEU* 2.8 35.3 + - + +
510B ALA 3.4 27.1 - - - +
511B MET* 3.7 10.1 - - - -
515B ARG* 3.7 4.7 - - - +
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Residues in contact with PHE 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LEU* 3.3 32.3 - - + -
413B SER* 3.4 22.4 - - - -
414B MET* 3.6 36.3 - - + -
417B ILE* 4.0 10.1 - - + -
439B PHE* 2.8 43.8 + + + +
440B GLU* 4.0 4.3 - - - +
442B ALA* 1.3 76.5 - - - +
444B LEU* 1.3 79.0 + - + +
446B LEU* 3.3 7.9 + - - +
447B PHE* 2.9 31.5 + - + +
591B LEU* 4.9 2.2 - - + -
601B 8SU 3.5 26.2 + - + +
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Residues in contact with LEU 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LEU* 4.1 15.5 - - + -
442B ALA 3.4 0.2 - - - -
443B PHE* 1.3 90.6 - - + +
445B GLU* 1.3 65.6 + - - +
447B PHE* 3.4 4.1 + - + +
448B VAL* 3.0 31.0 + - - +
482B TRP* 3.9 24.5 - - + -
566B CYS* 3.6 38.4 - - + +
569B GLY* 4.4 2.9 - - - -
570B LEU* 3.8 32.3 - - + +
573B ILE* 4.9 3.8 - - + -
601B 8SU 3.1 31.6 + - + +
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Residues in contact with GLU 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B SER 3.7 18.4 - - - +
442B ALA* 3.1 10.4 + - - +
444B LEU* 1.3 77.4 - - - +
446B LEU* 1.3 57.1 + - - +
448B VAL* 3.4 2.0 + - - -
449B LEU* 2.9 30.9 + - - +
510B ALA* 5.0 12.4 - - + +
515B ARG* 4.2 14.5 + - - -
559B LEU 3.9 6.2 - - - +
562B LEU* 3.4 55.0 - - + +
563B ARG* 3.7 12.4 + - - +
566B CYS* 3.8 10.5 - - + +
601B 8SU 4.2 8.0 - - - +
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Residues in contact with LEU 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B ILE* 3.7 26.5 - - + -
420B TRP* 3.6 29.4 - - + -
439B PHE* 4.9 2.2 - - + +
442B ALA* 2.8 41.3 + - + +
443B PHE* 3.7 5.2 - - - +
445B GLU* 1.3 69.4 - - - +
447B PHE* 1.3 61.1 + - - +
449B LEU* 4.4 5.2 - - + -
450B ARG* 2.9 40.8 + - - +
507B ALA* 3.2 36.3 - - + +
510B ALA* 4.0 11.4 - - + -
511B MET* 4.1 10.8 - - + -
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Residues in contact with PHE 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B LEU* 4.4 7.2 - - + -
410B LEU* 3.8 23.8 - - + -
413B SER* 3.4 33.0 - - - +
417B ILE* 3.7 9.6 - - + +
443B PHE* 2.9 23.0 + - + +
444B LEU* 3.6 6.5 - - + +
446B LEU* 1.3 75.4 - - - +
448B VAL* 1.3 76.4 + - + +
450B ARG* 4.3 1.9 - - - +
451B LEU* 3.2 47.7 + - + +
454B ARG* 5.1 4.9 + - - -
464B PHE* 4.2 16.4 - + - -
479B PHE* 3.9 28.0 - + - -
482B TRP* 3.8 21.8 - + - -
486B ILE* 4.5 1.6 - - + -
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Residues in contact with VAL 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B LEU 3.0 17.9 + - - +
445B GLU* 3.8 3.6 - - - +
447B PHE* 1.3 81.9 - - + +
449B LEU* 1.3 59.5 + - - +
451B LEU* 3.4 4.3 + - - +
452B ALA* 2.9 32.1 + - - +
482B TRP* 3.4 32.5 - - + +
486B ILE* 3.9 23.7 - - + +
489B PHE* 4.2 7.6 - - + -
562B LEU* 4.0 11.2 - - + -
565B LEU* 3.9 32.5 - - + +
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Residues in contact with LEU 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B GLU 2.9 18.0 + - - +
446B LEU* 3.9 6.3 - - + +
448B VAL* 1.3 77.4 - - - +
450B ARG* 1.3 63.3 + - + +
452B ALA* 3.4 5.1 + - - +
453B TYR* 3.1 24.4 + - - +
489B PHE* 4.2 17.0 - - + -
493B LEU* 4.2 12.5 - - + +
503B PHE* 3.6 24.6 - - + -
506B ILE* 4.4 14.4 - - + +
507B ALA* 3.6 37.0 - - + +
510B ALA* 4.8 4.7 - - + -
558B LYS* 5.4 2.5 - - + -
562B LEU* 3.8 29.1 - - + +
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Residues in contact with ARG 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B HIS* 4.6 2.8 - - + -
375B SER* 2.7 47.4 + - - -
376B ASN* 3.4 22.2 + - - +
416B ILE* 3.4 18.2 - - - +
417B ILE* 3.4 29.5 - - - +
420B TRP* 4.0 19.3 - - - +
446B LEU* 2.9 36.4 + - + +
447B PHE* 4.4 1.8 - - - +
449B LEU* 1.3 72.8 - - + +
451B LEU* 1.3 62.0 + - - +
453B TYR* 3.5 2.4 + - - +
454B ARG* 3.1 47.4 + - - +
465B CYS* 4.6 2.4 - - - +
503B PHE* 4.1 21.8 - - + -
507B ALA* 5.2 6.5 - - + -
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Residues in contact with LEU 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B PHE* 3.2 48.7 + - + +
448B VAL* 3.8 2.5 - - - +
450B ARG* 1.3 73.3 - - - +
452B ALA* 1.3 60.2 + - - +
454B ARG* 3.2 13.6 + - - +
455B SER* 2.6 51.1 + - - +
462B LEU* 4.0 14.1 - - + -
463B ILE 3.3 30.5 - - - +
464B PHE* 3.9 23.8 - - + -
479B PHE* 5.2 2.5 - - + -
483B ILE* 5.8 0.4 - - + -
486B ILE* 3.9 24.0 - - + -
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Residues in contact with ALA 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B VAL* 2.9 18.9 + - + +
449B LEU 3.6 4.7 - - - +
451B LEU* 1.3 78.6 - - - +
453B TYR* 1.3 55.9 + - - +
454B ARG 3.6 0.2 + - - -
455B SER* 3.9 1.2 + - - -
486B ILE* 4.6 5.4 - - + +
489B PHE* 3.6 29.8 - - + -
490B SER* 2.5 43.0 + - - +
493B LEU* 3.9 5.2 - - + -
494B GLN* 3.0 12.6 - - - +
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Residues in contact with TYR 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B HIS* 4.1 17.0 - + - -
449B LEU 3.1 18.0 + - - +
450B ARG 3.9 2.9 - - - +
451B LEU 3.3 0.2 - - - -
452B ALA* 1.3 77.2 - - - +
454B ARG* 1.3 58.7 + - - +
493B LEU* 3.8 17.7 - - + +
494B GLN* 3.3 20.8 - - + +
498B ILE* 2.5 39.4 + - + -
499B ASP 3.4 12.8 - - - -
500B ILE* 3.5 2.9 + - + -
503B PHE* 3.5 55.6 - + + -
370D ARG* 3.1 33.6 + - - -
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Residues in contact with ARG 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B ASN* 3.0 32.1 + - + -
377B PRO* 3.6 19.1 - - + +
379B MET* 3.7 20.3 - - - +
447B PHE* 5.1 4.8 + - - -
450B ARG* 3.1 35.6 + - - +
451B LEU* 3.6 22.1 - - - +
453B TYR* 1.3 76.0 - - - +
455B SER* 1.3 65.5 + - - +
463B ILE* 2.9 50.7 + - + +
464B PHE* 3.4 4.4 - - - +
465B CYS* 3.2 38.6 - - - +
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Residues in contact with SER 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B LEU* 2.6 31.4 + - - +
452B ALA* 3.9 0.8 + - - -
453B TYR 3.5 1.2 - - - -
454B ARG* 1.3 82.1 - - - +
456B ASN* 1.3 61.8 + - - +
457B PRO* 3.4 3.9 - - - +
461B LYS 3.1 13.5 - - - -
462B LEU* 3.4 8.0 - - - +
463B ILE* 3.1 25.6 + - - +
490B SER* 4.1 13.5 - - - -
494B GLN* 2.9 20.8 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il